NM_000404.4(GLB1):c.344del (p.Gly115fs) AND multiple conditions

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Sep 2, 2022
Review status:: 1 star out of maximum of 4 stars
criteria provided, single submitter

Somatic classification of clinical impact:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Somatic classification of oncogenicity:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Record status:: current
Accession:: RCV002876213.3

Allele description [Variation Report for NM_000404.4(GLB1):c.344del (p.Gly115fs)]

NM_000404.4(GLB1):c.344del (p.Gly115fs)

Gene:

GLB1:galactosidase beta 1 [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

3p22.3

Genomic location:

Preferred name:

NM_000404.4(GLB1):c.344del (p.Gly115fs)

HGVS:

NC_000003.12:g.33068874del
NG_009005.1:g.33331del
NG_009005.2:g.33274del
NM_000404.4:c.344delMANE SELECT
NM_001079811.3:c.254del
NM_001135602.3:c.246-3315del
NM_001317040.2:c.488del
NM_001393580.1:c.344del
NP_000395.3:p.Gly115fs
NP_001073279.2:p.Gly85fs
NP_001303969.2:p.Gly163fs
NP_001380509.1:p.Gly115fs
NC_000003.11:g.33110364del
NC_000003.11:g.33110366del

Protein change:

G115fs

Molecular consequence:

NM_000404.4:c.344del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001079811.3:c.254del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001317040.2:c.488del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001393580.1:c.344del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001135602.3:c.246-3315del - intron variant - [Sequence Ontology: SO:0001627]

Condition(s)

Name:: Mucopolysaccharidosis, MPS-IV-B (MPS4B)
Synonyms:: MPS IVB; Morquio syndrome B; MPS 4B; See all synonyms [MedGen]
Identifiers:: MONDO: MONDO:0009660; MedGen: C0086652; Orphanet: 582; OMIM: 253010

Name:: GM1 gangliosidosis
Synonyms:: Beta galactosidase 1 deficiency; GLB 1 deficiency
Identifiers:: MONDO: MONDO:0018149; MedGen: C0085131

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV003231066	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Sep 2, 2022)	germline	clinical testing	PubMed (2) [See all records that cite these PMIDs] 18524657, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV003231066

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Sep 2, 2022)

germline

clinical testing

PubMed (2)
[See all records that cite these PMIDs]

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

GM1 gangliosidosis: review of clinical, molecular, and therapeutic aspects.

Brunetti-Pierri N, Scaglia F.

Mol Genet Metab. 2008 Aug;94(4):391-396. doi: 10.1016/j.ymgme.2008.04.012. Epub 2008 Jun 3. Review.

PubMed [citation]

PMID:: 18524657

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV003231066.2

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (2)

Description

This sequence change creates a premature translational stop signal (p.Gly115Aspfs*6) in the GLB1 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in GLB1 are known to be pathogenic (PMID: 18524657). This variant is not present in population databases (gnomAD no frequency). For these reasons, this variant has been classified as Pathogenic. This variant has not been reported in the literature in individuals affected with GLB1-related conditions.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Sep 29, 2024

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